Commit 4ca5865c authored by Andreas Tille's avatar Andreas Tille

Tree-puzzle group maintenance

parents
tree-puzzle for Debian
----------------------
tree-puzzle replaces the previous package puzzle, since the program was
renamed by upstream because of a name conflict with another program.
The command and manpage for tree-puzzle are renamed to tree-puzzle as well!
Now also the parallelized version is packaged in the package tree-ppuzzle.
-- Andreas Tille <tille@debian.org> Mon, 5 Nov 2001 11:00:04 +0100
tree-puzzle (5.2-3) unstable; urgency=low
* Group maintenance according to Debian-Med group policy
* Do not auto generate debian/control
* Standards-Version: 3.7.3 (no changes needed)
* Removed XB-Tag which is not used
* Moved Homepage tag from description to control tags
* Removed [Biology] from short description
* Moved tree-puzzle-doc to section doc
* Added watch file
* debian/copyright: added Copyright statement
-- Andreas Tille <tille@debian.org> Sun, 02 Mar 2008 22:21:44 +0100
tree-puzzle (5.2-2) unstable; urgency=low
* Standards-Version: 3.7.2 (no changes necessary)
* Switched to cdbs
* Desktop file
* DebTags
* Build-Depends: lam4-dev to enable building parallelized version
* Split into two binary packages (normal and parallelized) version
and extra documentation package.
* Removed {Provides,Replaces,Conflicts}: puzzle because there is
no such package in the thre previous releases an it causes trouble
if both versions should be installed
-- Andreas Tille <tille@debian.org> Sun, 10 Sep 2006 18:13:50 +0200
tree-puzzle (5.2-1) unstable; urgency=low
* New upstream version
-- Andreas Tille <tille@debian.org> Thu, 15 Jul 2004 08:23:28 +0200
tree-puzzle (5.1-1) unstable; urgency=low
* New upstream version
* Standards: 3.6.1
* Enhanced use of debhelper scripts
-- Andreas Tille <tille@debian.org> Wed, 14 Jul 2004 10:03:31 +0200
tree-puzzle (5.0-4) unstable; urgency=low
* The "I'm against war" release
Mankind must put an end to war before war puts an end to mankind.
-- John F. Kennedy
* Standards-Version: 3.5.9
* Use debian/compat for debhelper compatibility
* Added documentation to doc-base
* Use dh_installman instead of dh_installmanpages
-- Andreas Tille <tille@debian.org> Sat, 26 Apr 2003 15:24:49 +0200
tree-puzzle (5.0-3) unstable; urgency=low
* New Maintainer
closes: #100265
* Standards-Version: 3.5.6
* Added URL to the package description because I consider this as
"good style" to have an upstream link without installing the package.
* Provides: puzzle
-- Andreas Tille <tille@debian.org> Mon, 5 Nov 2001 11:00:04 +0100
tree-puzzle (5.0-2) unstable; urgency=low
* Maintainer set to Debian QA Group <packages@qa.debian.org>.
-- Adrian Bunk <bunk@fs.tum.de> Fri, 24 Aug 2001 23:49:12 +0200
tree-puzzle (5.0-1) unstable; urgency=low
* Initial Release (replaces puzzle).
* Wrote a manpage.
-- Dr. Guenter Bechly <gbechly@debian.org> Sun, 6 May 2001 12:02:07 +0200
Source: tree-puzzle
Section: science
Priority: optional
Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <tille@debian.org>
Build-Depends: cdbs (>= 0.4.23-1.1), autotools-dev, patchutils (>= 0.2.25), debhelper (>= 4.2.0), debhelper (>= 4.2.21), lam4-dev
Standards-Version: 3.7.3
Homepage: http://www.tree-puzzle.de
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/tree-puzzle/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/tree-puzzle/trunk/
Package: tree-puzzle
Architecture: any
Depends: ${shlibs:Depends}
Recommends: tree-puzzle-doc
Suggests: phylip, treetool
Description: Reconstruction of phylogenetic trees by maximum likelihood
TREE-PUZZLE (the new name for PUZZLE) is an interactive console program that
implements a fast tree search algorithm, quartet puzzling, that allows
analysis of large data sets and automatically assigns estimations of support
to each internal branch. TREE-PUZZLE also computes pairwise maximum
likelihood distances as well as branch lengths for user specified trees.
Branch lengths can also be calculated under the clock-assumption. In
addition, TREE-PUZZLE offers a novel method, likelihood mapping, to
investigate the support of a hypothesized internal branch without
computing an overall tree and to visualize the phylogenetic content of
a sequence alignment.
Package: tree-ppuzzle
Architecture: any
Recommends: tree-puzzle-doc
Depends: ${shlibs:Depends}
Suggests: phylip, treetool
Description: Parallelized reconstruction of phylogenetic trees by maximum likelihood
TREE-PUZZLE (the new name for PUZZLE) is an interactive console program that
implements a fast tree search algorithm, quartet puzzling, that allows
analysis of large data sets and automatically assigns estimations of support
to each internal branch. TREE-PUZZLE also computes pairwise maximum
likelihood distances as well as branch lengths for user specified trees.
Branch lengths can also be calculated under the clock-assumption. In
addition, TREE-PUZZLE offers a novel method, likelihood mapping, to
investigate the support of a hypothesized internal branch without
computing an overall tree and to visualize the phylogenetic content of
a sequence alignment.
.
This is the parallelized version of tree-puzzle.
Package: tree-puzzle-doc
Architecture: all
Section: doc
Recommends: tree-puzzle | tree-ppuzzle
Description: Reconstruction of phylogenetic trees by maximum likelihood
TREE-PUZZLE (the new name for PUZZLE) is an interactive console program that
implements a fast tree search algorithm, quartet puzzling, that allows
analysis of large data sets and automatically assigns estimations of support
to each internal branch. TREE-PUZZLE also computes pairwise maximum
likelihood distances as well as branch lengths for user specified trees.
Branch lengths can also be calculated under the clock-assumption. In
addition, TREE-PUZZLE offers a novel method, likelihood mapping, to
investigate the support of a hypothesized internal branch without
computing an overall tree and to visualize the phylogenetic content of
a sequence alignment.
.
This is the documentation package for tree-puzzle
This package was debianized by -- Andreas Tille <tille@debian.org> on
Mon, 5 Nov 2001 11:00:04 +0100
It was downloaded from http://www.tree-puzzle.de
Upstream Authors: Korbinian Strimmer <korbinian.strimmer@zoo.ox.ac.uk>
and Arndt von Haeseler <haeseler@eva.mpg.de>.
Copyright 1995-1999 by Korbinian Strimmer and Arndt von Haeseler
Copyright 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron, and Arndt von Haeseler
Copyright 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler
License:
You are free to distribute this software under the terms of
the GNU General Public Licence.
On Debian systems, the complete text of the GNU General Public
Licence can be found in /usr/share/common-licenses/GPL file.
A small warning: some files are derived from a work (the book "Numerical
recipes") for which the authors do not hold the copyright. It does not
harm:
Date: Mon, 17 May 1999 13:08:31 +0200 (MET DST)
From: Korbinian Strimmer <strimmer@biochem.mpg.de>
To: Stephane Bortzmeyer <bortzmeyer@pasteur.fr>
Cc: Arndt von Haeseler <haeseler@eva.mpg.de>
Subject: License
[...]
However:
> >The whole package
> > is licenced under the GNU public licence, except for the parts
> > indicated in the sources where the copyright of the authors does not
> > apply.
>
> Grepping through the source code, I find no place where there is a
> copyright other than yours. Do you have the name of the other authors
> so we can reach them and try to see if they agree with a GPL
> distribution?
This means that parts of the sources originally derive from
Numerical Recipes (indicated in the sources). However, I think
that the code is suffiently modified as not be be generic
NR code. In addition, we are not making money with the program,
so probably the whole source can be considered GPL. On the
other hand, I have not asked NR and I am not a lawyer. For that
reason the GPL licence covers only part of the sources.
Korbinian
This diff is collapsed.
This diff is collapsed.
#!/usr/bin/make -f
# debian/rules for tree-puzzle using cdbs
# Andreas Tille <tille@debian.org>, GPL
pkg:=tree-puzzle
ppkg:=tree-ppuzzle
DEB_COMPRESS_EXCLUDE := .pdf .phy trees .b
## unfortunately this does not work :-(
# DEB_DH_INSTALLEXAMPLES_ARGS = --exclude Makefile*
## ... use regexp in tree-puzzle-doc.examples
include /usr/share/cdbs/1/rules/simple-patchsys.mk
include /usr/share/cdbs/1/rules/debhelper.mk
include /usr/share/cdbs/1/class/gnome.mk
clean::
## Work around a bug in the automake stuff of the upstream author ...
## src/sprng is not cleaned completely
# -cd src/sprng; $(MAKE) clean
## This worked formerly but once this is reached there is no
## Makefile anymore in place so ...
rm -f src/sprng/*.o
install/tree-puzzle::
# The binary has to be renamed because of the generic name
# cp -a src/puzzle `pwd`/debian/`dh_listpackages`/usr/bin/tree-puzzle
mv `pwd`/debian/tmp/usr/bin/puzzle `pwd`/debian/$(pkg)/usr/bin/$(pkg)
install/tree-ppuzzle::
# The binary has to be renamed because of the generic name
mv `pwd`/debian/tmp/usr/bin/ppuzzle `pwd`/debian/$(ppkg)/usr/bin/$(ppkg)
.TH TREE-PPUZZLE 1 "April 20, 2001"
.SH NAME
tree-ppuzzle \- Reconstruction of phylogenetic trees by maximum likelihood (parallelized version)
.SH SYNOPSIS
.B tree-ppuzzle
.RI
.SH DESCRIPTION
This manual page documents briefly the
.B tree-ppuzzle
command.
This manual page was written for the Debian GNU/Linux distribution
because the original program does not have a manual page.
.PP
TREE-PPUZZLE is the new name for the program previously known as PPUZZLE!
.PP
\fBtree-puzzle\fP is an interactive console program that implements a fast
tree search algorithm, quartet puzzling, that allows analysis of large
data sets and automatically assigns estimations of support to each
internal branch. TREE-PPUZZLE also computes pairwise maximum likelihood
distances as well as branch lengths for user specified trees. Branch
lengths can also be calculated under the clock-assumption. In
addition, TREE-PPUZZLE offers a novel method, likelihood mapping, to
investigate the support of a hypothesized internal branch without
computing an overall tree and to visualize the phylogenetic content of
a sequence alignment.
.PP
This program is the paralelized version of tree-puzzle.
.SH OPTIONS
There are no options. For usage please look at /usr/share/doc/tree-puzzle/tree-puzzle.pdf.
.SH SEE ALSO
.BR phylip (1),
.BR treetool (1).
.BR tree-puzzle (1).
.PP
This manual page was written by Dr. Guenter Bechly <gbechly@debian.org>,
for the Debian GNU/Linux system (but may be used by others).
[Desktop Entry]
Version=1.0
Encoding=UTF-8
Terminal=true
Icon=tree-ppuzzle
Exec=tree-ppuzzle
Name=tree-ppuzzle
GenericName=Reconstruction of phylogenetic trees (parallelized)
GenericName[en]=Reconstruction of phylogenetic trees (parallelized)
Comment=Reconstruction of phylogenetic trees by maximum likelihood (parallelized version)
Comment[en]=Reconstruction of phylogenetic trees by maximum likelihood (parallelized version)
Type=Application
Categories=Biology;Science;Education;
debian/README.Debian
debian/tree-ppuzzle.desktop usr/share/applications
debian/tree-ppuzzle.xpm usr/share/pixmaps
debian/tree-ppuzzle.1
/* XPM */
static char *tree-ppuzzle[] = {
/* columns rows colors chars-per-pixel */
"32 32 2 1",
" c black",
". c #0099FF",
/* pixels */
" ",
" ...... ....... ...... ....... ",
" . . . . . . . . ",
" . .. ..... . .. ..... ",
" .... .. .. . . .... .. .. . . ",
" . . . . . . . . ",
" .. . . ....... .. . . ....... ",
" . ..... . . ..... . ",
" .. . ..... .. . ..... ",
" . ... . . . ... . . ",
" .... . ... ... .... . ... ... ",
" . . . . . . . . ",
" .. ... ... ... .. ... ... ... ",
" . . . . . . . . ",
" . .... ... ... . .... ... ... ",
" ",
" ",
" ...... ....... ...... ....... ",
" . . . . . . . . ",
" . .. ..... . .. ..... ",
" .... .. .. . . .... .. .. . . ",
" . . . . . . . . ",
" .. . . ....... .. . . ....... ",
" . ..... . . ..... . ",
" .. . ..... .. . ..... ",
" . ... . . . ... . . ",
" .... . ... ... .... . ... ... ",
" . . . . . . . . ",
" .. ... ... ... .. ... ... ... ",
" . . . . . . . . ",
" . .... ... ... . .... ... ... ",
" "
};
Document: tree-puzzle
Title: TREE-PUZZLE Manual
Author: Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron, Arndt von Haeseler
Abstract: Maximum likelihood analysis for nucleotide, amino acid, and two-state
data
Section: Apps/Science
Format: pdf
Files: /usr/share/doc/tree-puzzle-doc/tree-puzzle.pdf
AUTHORS
README
doc/*.html
doc/*.pdf
.TH TREE-PUZZLE 1 "April 20, 2001"
.SH NAME
tree-puzzle \- Reconstruction of phylogenetic trees by maximum likelihood
.SH SYNOPSIS
.B tree-puzzle
.RI
.SH DESCRIPTION
This manual page documents briefly the
.B tree-puzzle
command.
This manual page was written for the Debian GNU/Linux distribution
because the original program does not have a manual page.
.PP
TREE-PUZZLE is the new name for the program previously known as PUZZLE!
.PP
\fBtree-puzzle\fP is an interactive console program that implements a fast
tree search algorithm, quartet puzzling, that allows analysis of large
data sets and automatically assigns estimations of support to each
internal branch. TREE-PUZZLE also computes pairwise maximum likelihood
distances as well as branch lengths for user specified trees. Branch
lengths can also be calculated under the clock-assumption. In
addition, TREE-PUZZLE offers a novel method, likelihood mapping, to
investigate the support of a hypothesized internal branch without
computing an overall tree and to visualize the phylogenetic content of
a sequence alignment.
.PP
There is also a paralellized version tree-ppuzzle available.
.SH OPTIONS
There are no options. For usage please look at /usr/share/doc/tree-puzzle/tree-puzzle.pdf.
.SH SEE ALSO
.BR phylip (1),
.BR treetool (1).
.BR tree-ppuzzle (1).
.PP
This manual page was written by Dr. Guenter Bechly <gbechly@debian.org>,
for the Debian GNU/Linux system (but may be used by others).
[Desktop Entry]
Version=1.0
Encoding=UTF-8
Terminal=yes
Icon=tree-puzzle
Exec=tree-puzzle
Name=tree-puzzle
GenericName=Reconstruction of phylogenetic trees
GenericName[en]=Reconstruction of phylogenetic trees
Comment=Reconstruction of phylogenetic trees by maximum likelihood
Comment[en]=Reconstruction of phylogenetic trees by maximum likelihood
Type=Application
Categories=Biology;Science;Education;
debian/README.Debian
debian/tree-puzzle.desktop usr/share/applications
debian/tree-puzzle.xpm usr/share/pixmaps
debian/tree-puzzle.1
/* XPM */
static char *puzzle[] = {
/* columns rows colors chars-per-pixel */
"32 32 2 1",
" c black",
". c #0098F8",
/* pixels */
" ",
" ",
" ............ .............. ",
" ............ .............. ",
" .. .. .. .. ",
" .. .. .. .. ",
" .. .... .......... ",
" .. .... .......... ",
" ........ .... .... .. .. ",
" ........ .... .... .. .. ",
" .. .. .. .. ",
" .. .. .. .. ",
" .... .. .. .............. ",
" .... .. .. .............. ",
" .. .......... .. ",
" .. .......... .. ",
" .... .. .......... ",
" .... .. .......... ",
" .. ...... .. .. ",
" .. ...... .. .. ",
" ........ .. ...... ...... ",
" ........ .. ...... ...... ",
" .. .. .. .. ",
" .. .. .. .. ",
" .... ...... ...... ...... ",
" .... ...... ...... ...... ",
" .. .. .. .. ",
" .. .. .. .. ",
" .. ........ ...... ...... ",
" .. ........ ...... ...... ",
" ",
" "
};
version=3
http://www.tree-puzzle.de/tree-puzzle-([.0-9]*)\.tar\.gz
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment